The 34-year-old's name did not feature among the four nominees for the coveted 'Test Cricketer of the Year' award, despite being Test cricket's leading wicket-taker in the period under consideration.
South Africa's Hashim Amla and Vernon Philander, Sri Lanka's Kumar Sangakkara and Australia's Michael Clarke all made the list.
The International Cricket Council (ICC) holds the annual awards ceremony to recognise the best players and umpire in international cricket.
The names are chosen by a 30-member jury comprising of former players, officials and journalists. This year's ceremony will be held in Colombo on September 15.
Ajmal took 72 wickets in the 12 month period, including 24 in Pakistan's 3-0 rout of then world number one Test team England earlier this year.
PCB spokesman Nadeem Sarwar said they have written to the ICC on Ajmal's omission.
"Yes, we have shown our concerns on Ajmal's name not shortlisted for Test player of the year award despite his excellent performance in Tests during that stipulated period," Sarwar told AFP.
"We hope that the ICC will reconsider this and include Ajmal's name," he added.
Graeme Swann was omitted from a shortlist in 2010 but was later included after England put up his case. South Africa also objected to the omission of their players and boycotted the 2009 ceremony held in Johannesburg.
Despite his omission from the award shortlist, Ajmal's name has been included in ICC's best Test team of the year.
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@Vickram Buckup boy! ur jealousy reached new heights ...
@vickram: At least PAK has bowlers as part of its playing 11 ;)
Maybe, the list is only for bowlers with clean action....
No Doubt Ajmal is a legend ....... PCB should also boycott the ceremony
Seriously? What was jury thinking while omitting him??